data_3SEK # _model_server_result.job_id PLwm2oSK59qg-C83UcYJ9A _model_server_result.datetime_utc '2024-11-29 15:54:53' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3sek # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1}' # _entry.id 3SEK # _exptl.entry_id 3SEK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 3SEK _cell.length_a 82.086 _cell.length_b 82.086 _cell.length_c 312.691 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SEK _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 12_565 x,x-y+1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -41.043 71.088561 52.115167 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 6 B CYS 6 1_555 A SG CYS 16 B CYS 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 A SG CYS 15 B CYS 15 1_555 A SG CYS 74 B CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 A SG CYS 43 B CYS 43 1_555 A SG CYS 106 B CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 47 B CYS 47 1_555 A SG CYS 108 B CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf5 A SG CYS 73 B CYS 73 1_555 A SG CYS 73 B CYS 73 12_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? disulf ? disulf6 B SG CYS 3 C CYS 12 1_555 B SG CYS 26 C CYS 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf7 B SG CYS 13 C CYS 22 1_555 B SG CYS 57 C CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf8 B SG CYS 27 C CYS 36 1_555 B SG CYS 60 C CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf9 B SG CYS 64 C CYS 73 1_555 B SG CYS 75 C CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf10 B SG CYS 69 C CYS 78 1_555 B SG CYS 84 C CYS 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf11 B SG CYS 86 C CYS 95 1_555 B SG CYS 118 C CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf12 B SG CYS 90 C CYS 99 1_555 B SG CYS 111 C CYS 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 B SG CYS 100 C CYS 109 1_555 B SG CYS 132 C CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf14 B SG CYS 136 C CYS 145 1_555 B SG CYS 147 C CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf15 B SG CYS 141 C CYS 150 1_555 B SG CYS 157 C CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf16 B SG CYS 160 C CYS 169 1_555 B SG CYS 194 C CYS 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf17 B SG CYS 165 C CYS 174 1_555 B SG CYS 187 C CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf18 B SG CYS 176 C CYS 185 1_555 B SG CYS 208 C CYS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 C C1 NAG . C NAG 1 1_555 B ND2 ASN 38 C ASN 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 C2 NAG sing 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 3SEK _atom_sites.fract_transf_matrix[1][1] 0.012182 _atom_sites.fract_transf_matrix[1][2] 0.007033 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014067 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.003198 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 NAG C 1 1 1 NAG NAG . D 4 HOH B 1 110 1 HOH HOH . D 4 HOH B 2 111 3 HOH HOH . D 4 HOH B 3 112 4 HOH HOH . D 4 HOH B 4 113 5 HOH HOH . D 4 HOH B 5 114 7 HOH HOH . D 4 HOH B 6 115 8 HOH HOH . D 4 HOH B 7 116 10 HOH HOH . D 4 HOH B 8 117 15 HOH HOH . D 4 HOH B 9 118 17 HOH HOH . D 4 HOH B 10 119 18 HOH HOH . D 4 HOH B 11 120 20 HOH HOH . D 4 HOH B 12 121 21 HOH HOH . D 4 HOH B 13 122 22 HOH HOH . D 4 HOH B 14 123 25 HOH HOH . D 4 HOH B 15 124 27 HOH HOH . D 4 HOH B 16 125 28 HOH HOH . D 4 HOH B 17 126 29 HOH HOH . D 4 HOH B 18 127 30 HOH HOH . D 4 HOH B 19 128 32 HOH HOH . D 4 HOH B 20 129 35 HOH HOH . D 4 HOH B 21 130 36 HOH HOH . D 4 HOH B 22 131 37 HOH HOH . D 4 HOH B 23 132 40 HOH HOH . D 4 HOH B 24 133 42 HOH HOH . D 4 HOH B 25 134 50 HOH HOH . D 4 HOH B 26 135 51 HOH HOH . D 4 HOH B 27 136 52 HOH HOH . D 4 HOH B 28 137 53 HOH HOH . D 4 HOH B 29 138 54 HOH HOH . D 4 HOH B 30 139 55 HOH HOH . D 4 HOH B 31 140 57 HOH HOH . D 4 HOH B 32 141 58 HOH HOH . E 4 HOH C 1 2 2 HOH HOH . E 4 HOH C 2 6 6 HOH HOH . E 4 HOH C 3 9 9 HOH HOH . E 4 HOH C 4 219 11 HOH HOH . E 4 HOH C 5 220 12 HOH HOH . E 4 HOH C 6 221 13 HOH HOH . E 4 HOH C 7 222 14 HOH HOH . E 4 HOH C 8 223 16 HOH HOH . E 4 HOH C 9 224 23 HOH HOH . E 4 HOH C 10 225 24 HOH HOH . E 4 HOH C 11 226 26 HOH HOH . E 4 HOH C 12 227 31 HOH HOH . E 4 HOH C 13 228 33 HOH HOH . E 4 HOH C 14 229 34 HOH HOH . E 4 HOH C 15 230 38 HOH HOH . E 4 HOH C 16 231 39 HOH HOH . E 4 HOH C 17 232 41 HOH HOH . E 4 HOH C 18 233 43 HOH HOH . E 4 HOH C 19 234 44 HOH HOH . E 4 HOH C 20 235 45 HOH HOH . E 4 HOH C 21 236 46 HOH HOH . E 4 HOH C 22 237 47 HOH HOH . E 4 HOH C 23 238 48 HOH HOH . E 4 HOH C 24 239 49 HOH HOH . E 4 HOH C 25 240 56 HOH HOH . E 4 HOH C 26 241 59 HOH HOH . E 4 HOH C 27 242 60 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 NAG . . . C 3 -15.733 6.614 48.333 1 59.24 ? C1 NAG 1 C 1 HETATM 2 C C2 NAG . . . C 3 -15.119 5.236 48.057 1 66.38 ? C2 NAG 1 C 1 HETATM 3 C C3 NAG . . . C 3 -15.868 4.189 48.89 1 67.83 ? C3 NAG 1 C 1 HETATM 4 C C4 NAG . . . C 3 -15.75 4.535 50.379 1 68.34 ? C4 NAG 1 C 1 HETATM 5 C C5 NAG . . . C 3 -16.226 5.978 50.65 1 67.26 ? C5 NAG 1 C 1 HETATM 6 C C6 NAG . . . C 3 -15.921 6.409 52.092 1 68.07 ? C6 NAG 1 C 1 HETATM 7 C C7 NAG . . . C 3 -14.017 4.819 45.888 1 69.74 ? C7 NAG 1 C 1 HETATM 8 C C8 NAG . . . C 3 -14.214 4.436 44.447 1 69.62 ? C8 NAG 1 C 1 HETATM 9 N N2 NAG . . . C 3 -15.127 4.888 46.639 1 68.15 ? N2 NAG 1 C 1 HETATM 10 O O3 NAG . . . C 3 -15.387 2.878 48.641 1 69.02 ? O3 NAG 1 C 1 HETATM 11 O O4 NAG . . . C 3 -16.475 3.582 51.141 1 70.04 ? O4 NAG 1 C 1 HETATM 12 O O5 NAG . . . C 3 -15.634 6.908 49.731 1 64.5 ? O5 NAG 1 C 1 HETATM 13 O O6 NAG . . . C 3 -16.833 7.399 52.533 1 69.31 ? O6 NAG 1 C 1 HETATM 14 O O7 NAG . . . C 3 -12.878 5.053 46.311 1 70.42 ? O7 NAG 1 C 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #